Partial alignment and measurement of residual dipolar couplings of proteins under high hydrostatic pressure

High-pressure NMR spectroscopy has emerged as a complementary approach for investigating various structural and thermodynamic properties of macromolecules. Noticeably absent from the array of experimental restraints that have been employed to characterize protein structures at high hydrostatic pressure is the residual dipolar coupling, which requires the partial alignment of the macromolecule of interest. Here we examine five alignment media that are commonly used at ambient pressure for this purpose. We find that the spontaneous alignment of Pf1 phage, d(GpG) and a C12E5/n-hexnanol mixture in a magnetic field is preserved under high hydrostatic pressure. However, DMPC/ DHPC bicelles and collagen gel are found to be unsuitable. Evidence is presented to demonstrate that pressure-induced structural changes can be identified using the residual dipolar coupling

Dynamic nature of proteins : interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.Proteiinit ovat elämän kannalta välttämättömiä molekyylejä. Solujen toiminta perustuu pitkälti proteiineihin, joita solut valmistavat DNA:ssa olevien "rakennusohjeiden" mukaisesti. Proteiineihin liittyvät häiriöt ovat syypää mm. sellaisiin vakaviin saurauksiin kuin Alzheimerin ja Creutzfeldt-Jakobin taudit. Proteiineilla on yleensä hyvin määritelty ja kohtuullisen vakaa rakenne, mutta usein proteiini sisältää myös heikosti rakenteellisia osia. On olemassa myös rakenteellisesti epävakaita proteiineja, jotka ottavat toiminnallisen muotonsa vasta vuorovaikutuksessa. Kaikki proteiinit ovat kuitenkin jatkuvassa sisäisessä liikkeessä; niiden muoto elää alati. Tässä työssä on tutkittu proteiinien rakenteellisten ja dynaamisten ominaisuuksien tulkintaa ydinmagneettisella resonanssispektroskopialla mitatuista tuloksista. Siinä on osoitettu, että vastoin aiempaa käsitystä myös täysin rakenteettomista proteiineista saadaan mitattua jäännösdipolikytkennäksi kutsuttu suure, joka antaa ainutlaatuista tietoa molekyylin atomien välisistä suhteista. Työssä on myös osoitettu riittämättömäksi vallitseva tapa kohdella proteiinia kuin kiinteää molekyyliä sen keskimääräistä asentoa määritettäessä. Tutkimuksen tulokset mahdollistavat entistä tarkemman kuvan saamisen proteiinien rakenteellisista ja dynaamisista ominaisuuksista. Proteiinien ominaisuuksien lisääntynyt ymmärrys voi mahdollistaa mm. entistä tehokkaampien lääkeaineiden suunnittelun ja kehittämisen

The Flexibility of Oligosaccharides Unveiled Through Residual Dipolar Coupling Analysis

The intrinsic flexibility of glycans complicates the study of their structures and dynamics, which are often important for their biological function. NMR has provided insights into the conformational, dynamic and recognition features of glycans, but suffers from severe chemical shift degeneracy. We employed labelled glycans to explore the conformational behaviour of a β(1-6)-Glc hexasaccharide model through residual dipolar couplings (RDCs). RDC delivered information on the relative orientation of specific residues along the glycan chain and provided experimental clues for the existence of certain geometries. The use of two different aligning media demonstrated the adaptability of flexible oligosaccharide structures to different environments

Measurement of Untruncated Nuclear Spin Interactions via Zero- to Ultra-Low-Field Nuclear Magnetic Resonance

Zero- to ultra-low-field nuclear magnetic resonance (ZULF NMR) provides a new regime for the measurement of nuclear spin-spin interactions free from effects of large magnetic fields, such as truncation of terms that do not commute with the Zeeman Hamiltonian. One such interaction, the magnetic dipole-dipole coupling, is a valuable source of spatial information in NMR, though many terms are unobservable in high-field NMR, and the coupling averages to zero under isotropic molecular tumbling. Under partial alignment, this information is retained in the form of so-called residual dipolar couplings. We report zero- to ultra-low-field NMR measurements of residual dipolar couplings in acetonitrile-2-$^{13}$C aligned in stretched polyvinyl acetate gels. This represents the first investigation of dipolar couplings as a perturbation on the indirect spin-spin $J$-coupling in the absence of an applied magnetic field. As a consequence of working at zero magnetic field, we observe terms of the dipole-dipole coupling Hamiltonian that are invisible in conventional high-field NMR. This technique expands the capabilities of zero- to ultra-low-field NMR and has potential applications in precision measurement of subtle physical interactions, chemical analysis, and characterization of local mesoscale structure in materials.Comment: 6 pages, 3 figure

Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range

High-resolution NMR studies of solid halogenated organic compounds

This thesis is a study of solid halogenated organic compounds by Nuclear Magnetic Resonance Spectroscopy (NMR) in an attempt to extract previously inaccessible information. The first part of the thesis is concerned with three fluorinated steroids, studied by observing (^1)H, (^13)C and (^19)F nuclei. A number of experimental techniques are employed to verify solution-state and solid-state spectral assignments, and spectral anomalies are discussed. Both proton-coupled and proton-decoupled (^19)F solid-state spectra, recorded using specially designed spectrometer hardware, are presented. The huge gain in resolution afforded by the implementation of proton decoupling allows static and MAS spectra to yield previously inaccessible information pertaining to various NMR parameters of the fluorine nuclei. Advantages of (^1)H→(^19)F cross-polarisation experiments over single-pulse experiments are explained and rotational resonance, dipolar dephasing, T(_1), measurement and spin-exchange experiments are presented from which information regarding phenomena such as spin diffusion and polymorphism is gleaned. The second part of the thesis focusses on the topic of residual dipolar coupling, the transfer of quadrupolar effects to spin-1/2 nuclei via dipolar coupling and/or anisotropy m indhect coupling. Unexpected, field-dependent, multiplicities for signals in spectra of spin-1/2 nuclei are observed, which can be used to evaluate certain fundamental NMR parameters including the quadrupolar coupling constant and, m favourable cases, anisotropy in indirect coupling. The phenomenon is comprehensively studied for the (^13)C, (^35,37)Cl and (^13)C, (^79,81)Br spin-pairs in a range of solid halogenated compounds. Coupling to more than one halogen nucleus and long- range (non-bonded) coupling are considered. First-order perturbation, inverse first- order and "exact" theories, that allow the multiplet line positions to be predicted, are introduced and their results are subsequently compared to the experimentally observed the positions. Rapid molecular motion is shown to negate the effects of residual dipolar coupling and the phenomenon is analysed with the aid of NQR measurements